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- Title
Small RNAs in angiosperms: sequence characteristics, distribution and generation.
- Authors
Dijun Chen; Yijun Meng; Xiaoxia Ma; Chuanzao Mao; Youhuang Bai; Junjie Cao; Haibin Gu; Ping Wu; Ming Chen
- Abstract
High-throughput sequencing (HTS) has opened up a new era for small RNA (sRNA) exploration. Using HTS data for a global survey of sRNAs in 26 angiosperms, elevated GC contents were detected in the monocots, whereas the 5′-terminal compositions were quite uniform among the angiosperms. Chromosome-wide distribution patterns of sRNAs were investigated by using scrolling-window analysis. We performed de novo natural antisense transcript (NAT) prediction, and found that the overlapping regions of trans-NATs, but not cis-NATs, were hotspots for sRNA generation. One cis-NAT generates phased natural antisense short interfering RNAs (nat-siRNAs) specifically from flowers in Arabidopsis, while one in rice produces phased nat-siRNAs from grains, suggesting their organ-specific regulatory roles.
- Subjects
ANGIOSPERMS; PLANT genetics; NON-coding RNA; PLANT chromosomes; PLANT cells &; tissues
- Publication
Bioinformatics, 2010, Vol 26, Issue 11, p1391
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btq150